[mira_talk] Re: Install Mira on 10.7.5
- From: Shaun Jackman <sjackman@xxxxxxxxx>
- To: George Tsiamis <gtsiamis1@xxxxxxxxx>
- Date: Sun, 28 Oct 2012 13:40:32 -0700
Hi George,
My patch is incorporated into the main homebrew repository now, so it
should work out of the box now:
brew install homebrew
Cheers,
Shaun
On 28 October 2012 13:36, Shaun Jackman <sjackman@xxxxxxxxx> wrote:
> Hi George,
>
> Sorry for the bad link. That should have been
>
> brew install
> https://raw.github.com/sjackman/homebrew/mira/Library/Formula/mira.rb
>
> Cheers,
> Shaun
>
> On 23 October 2012 09:21, George Tsiamis <gtsiamis1@xxxxxxxxx> wrote:
>> Hi Shaun,
>>
>> I tried the command that you mention and now I am getting
>>
>> pc-5:GT_Files gtsiamis$ brew install
>> http://github.com/sjackman/homebrew/blob/mira/Library/Formula/mira.rb
>> ########################################################################
>> 100.0%
>> Error: /Library/Caches/Homebrew/Formula/mira.rb:4: syntax error, unexpected
>> '<'
>> <!DOCTYPE html>
>> ^
>> /Library/Caches/Homebrew/Formula/mira.rb:5: syntax error, unexpected '<'
>> <html>
>> ^
>> /Library/Caches/Homebrew/Formula/mira.rb:7: syntax error, unexpected '<'
>> <meta charset='utf-8'>
>> ^
>> /Library/Caches/Homebrew/Formula/mira.rb:8: syntax error, unexpected '<'
>> <meta http-equiv="X-UA-Compatible" content="IE=edge">
>> ^
>> /Library/Caches/Homebrew/Formula/mira.rb:8: syntax error, unexpected
>> tIDENTIFIER, expecting $end
>> <meta http-equiv="X-UA-Compatible" content="IE=edge">
>> ^
>> Please report this bug:
>> https://github.com/mxcl/homebrew/wiki/troubleshooting
>> /usr/local/Library/Homebrew/formula.rb:396:in `require'
>> /usr/local/Library/Homebrew/formula.rb:396:in `factory'
>> /usr/local/Library/Homebrew/extend/ARGV.rb:20:in `formulae'
>> /usr/local/Library/Homebrew/extend/ARGV.rb:20:in `map'
>> /usr/local/Library/Homebrew/extend/ARGV.rb:20:in `formulae'
>> /usr/local/Library/Homebrew/cmd/install.rb:21:in `install'
>> /usr/local/bin/brew:94:in `send'
>> /usr/local/bin/brew:94
>>
>>
>> Any suggestions
>>
>> George
>>
>>
>>
>>
>> George Tsiamis, Ph.D.
>> Lecturer in Environmental Microbiology
>> Department of Environmental and Natural Resources Management
>> University of Western Greece
>> 2 Seferi str., Agrinio
>> 30100, Greece
>> e-mail: gtsiamis@xxxxxxxxx, gtsiamis1@xxxxxxxxx, gtsiamis@xxxxxx
>> tel. +302641074149, fax. +302641074171
>>
>> On Oct 23, 2012, at 7:13 PM, Shaun Jackman wrote:
>>
>>> Hi George,
>>>
>>> I'm working on updating MIRA in homebrew. Try
>>> brew install
>>> http://github.com/sjackman/homebrew/blob/mira/Library/Formula/mira.rb
>>>
>>> Cheers,
>>> Shaun
>>>
>>> On 22 October 2012 23:50, George Tsiamis <gtsiamis1@xxxxxxxxx> wrote:
>>>> Hi Shaun,
>>>>
>>>> Thanks for the Homebrew tip and above all your quick reply.
>>>>
>>>> I just installed Homebrew and run
>>>>
>>>> brew install mira
>>>>
>>>> What I get now is
>>>>
>>>> ==> Downloading
>>>> http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira-3.4.0.1.ta
>>>>
>>>> curl: (22) The requested URL returned error: 404
>>>> Error: Download failed:
>>>> http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira-3.4.0.1.tar.bz2
>>>>
>>>>
>>>> I think the problem is that at the source forge they have the
>>>> 3.4.0.2version and not the 3.4.0.1
>>>>
>>>> How we can sort this out?
>>>>
>>>> Thanks in advance
>>>>
>>>> george
>>>>
>>>>
>>>>
>>>>
>>>> George Tsiamis, Ph.D.
>>>> Lecturer in Environmental Microbiology
>>>> Department of Environmental and Natural Resources Management
>>>> University of Western Greece
>>>> 2 Seferi str., Agrinio
>>>> 30100, Greece
>>>> e-mail: gtsiamis@xxxxxxxxx, gtsiamis1@xxxxxxxxx, gtsiamis@xxxxxx
>>>> tel. +302641074149, fax. +302641074171
>>>>
>>>> On Oct 23, 2012, at 9:24 AM, Shaun Jackman wrote:
>>>>
>>>>> Hi George,
>>>>>
>>>>> You must link against boost_system:
>>>>> make LIBS=-lboost_system-mt
>>>>>
>>>>> Try Homebrew:
>>>>> brew install mira
>>>>>
>>>>> Cheers,
>>>>> Shaun
>>>>>
>>>>> On 2012-10-22, at 23:18, George Tsiamis <gtsiamis1@xxxxxxxxx> wrote:
>>>>>
>>>>>> Dear all,
>>>>>>
>>>>>>
>>>>>> I am trying to install Mira stable version 3.4.0.2 on my Mac running
>>>>>> Lion 10.7.5. I have used macports to install gcc4.7, boost, expat, and
>>>>>> flex.
>>>>>>
>>>>>> The commands that I give are:
>>>>>>
>>>>>> ./configure --with-tcmalloc=yes
>>>>>>
>>>>>> At the end of the configure I get
>>>>>>
>>>>>> --------------------------------------------------------------------------------
>>>>>> Summary of MIRA configuration
>>>>>> --------------------------------------------------------------------------------
>>>>>>
>>>>>> Linking against tcmalloc is disabled!
>>>>>> Note that is the default for OS X, but you might want to try switching
>>>>>> it on like this: --with-tcmalloc
>>>>>>
>>>>>> Building version .................................
>>>>>> 3.4.0.2_prod_darwin11.4.2_x86_64_dynamic
>>>>>> Production or development version?................ production
>>>>>>
>>>>>> We are building on ............................... Darwin
>>>>>> CPU supports 64 bit? ......... ................... yes
>>>>>> Compiler ......................................... gcc
>>>>>> Compiler optimisation flags used ................. -O3 -funroll-loops
>>>>>> Do we compile in 64 bit? ......................... yes
>>>>>> Building completely static? ...................... no
>>>>>> BOOST expected to compile and link?............... yes
>>>>>> Linking with TCmalloc library?.................... no
>>>>>>
>>>>>> Can MIRA be built on this system? ................ yes
>>>>>>
>>>>>> Using CFLAGS : -mmacosx-version-min=10.5 -O3 -funroll-loops
>>>>>> -I/usr/local/include
>>>>>> Using CXXFLAGS : -DPUBLICQUIET -mmacosx-version-min=10.5 -O3
>>>>>> -funroll-loops -I/usr/local/include -pthread -I/opt/local/include
>>>>>> Using LDFLAGS : -L/opt/local/lib -lboost_thread-mt -lboost_regex-mt
>>>>>>
>>>>>> Looks good, we do not expect compilation problems.
>>>>>> --------------------------------------------------------------------------------
>>>>>>
>>>>>> Type 'make' to make the binaries
>>>>>> and then 'make install' to install them.
>>>>>>
>>>>>> But then when I type "make" I get
>>>>>>
>>>>>> Undefined symbols for architecture x86_64:
>>>>>> "boost::system::system_category()", referenced from:
>>>>>> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein mira_101.o
>>>>>> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein
>>>>>> libmira.a(assembly.o)
>>>>>> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein
>>>>>> libmira.a(assembly_io.o)
>>>>>> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein
>>>>>> libmira.a(newpathfinder.o)
>>>>>> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein libmira.a(skim.o)
>>>>>> boost::mutex::lock() in libmira.a(skim.o)
>>>>>> boost::unique_lock<boost::mutex>::lock() in libmira.a(skim.o)
>>>>>> ...
>>>>>> "boost::system::generic_category()", referenced from:
>>>>>> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein mira_101.o
>>>>>> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein
>>>>>> libmira.a(assembly.o)
>>>>>> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein
>>>>>> libmira.a(assembly_io.o)
>>>>>> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein
>>>>>> libmira.a(newpathfinder.o)
>>>>>> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein libmira.a(skim.o)
>>>>>> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein
>>>>>> libmira.a(assembly_swalign.o)
>>>>>> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein
>>>>>> libmira.a(assembly_reduceskimhits.o)
>>>>>> ...
>>>>>> ld: symbol(s) not found for architecture x86_64
>>>>>> collect2: ld returned 1 exit status
>>>>>> make[2]: *** [mira_101] Error 1
>>>>>> make[1]: *** [all-recursive] Error 1
>>>>>> make: *** [all-recursive] Error 1
>>>>>>
>>>>>> and I am stuck here.
>>>>>>
>>>>>> I do not know what I can try next to overcome thisâ.
>>>>>>
>>>>>> Any suggestions?
>>>>>>
>>>>>> Thanks in advance
>>>>>>
>>>>>> George
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> George Tsiamis, Ph.D.
>>>>>> Lecturer in Environmental Microbiology
>>>>>> Department of Environmental and Natural Resources Management
>>>>>> University of Western Greece
>>>>>> 2 Seferi str., Agrinio
>>>>>> 30100, Greece
>>>>>> e-mail: gtsiamis@xxxxxxxxx, gtsiamis1@xxxxxxxxx, gtsiamis@xxxxxx
>>>>>> tel. +302641074149, fax. +302641074171
>>>>>>
>>>>>>
>>>>>> --
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>>>>
>>
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